Patent Application
20130309674
The present invention relates to the diagnosis of Parkinson's disease, especially to the diagnosis of sporadic Parkinson's disease. The present invention relates to the use of peripheral blood monocytes for determining the methylation status of the human alpha-synuclein gene for diagnosing Parkinson's disease and/or for assessing a patient's risk of developing Parkinson's disease. The present invention further provides a method for determining methylation of the human alpha-synuclein gene in peripheral blood monocytes for diagnosing Parkinson's disease and/or for assessing a patient's risk of developing Parkinson's disease. The present invention also provides a method for diagnosing Parkinson's disease and/or for assessing a patient's risk of developing Parkinson's disease
Parkinson's disease (“PD”) is one of the most common neurodegenerative diseases. Approximately 2% of elderly persons (older than 65) are affected. The clinical symptoms of PD are characterized by akinetic-rigid motor dysfunction and cognitive, affective and neurobehavioural impairments. The most prominent neuropathological characteristics of Parkinson's disease are progressive cell death within the nigro-striatal dopaminergic system, and the appearance of cytoplasmic protein aggregates, the so-called Lewy bodies, in cells of the central nervous system of affected persons.
The majority of PD cases occur sporadically, and its etiology is largely unknown. Pursuant to recent findings, PD is usually diagnosed in an advanced stage of the disease. A neuro-protective or neuro-restorative therapy can therefore only be launched late in the disease's progression. Current methods of diagnosing PD, for example, single photon emission computed tomography (SPECT) or positron emission tomography (PET), are expensive and are therefore only used subsequent to clinical presumption diagnosis or for differential diagnosis. Although some symptoms such as sensory and sleep difficulties are discussed as useful in early diagnosis of PD, they are not specific enough and lack sensitivity. A simple to perform and inexpensive test for determining the risk of being affected by PD is not yet available.
According to its pathophysiology, PD may be considered a synucleinopathy due to the abnormal accumulation of the alpha-synuclein (SNCA) protein in the brain of patients having developed PD. Since the alpha-synuclein protein is the main component of Lewy bodies, a number of specific genetic mutations of the alpha-synuclein gene associated with PD have been discovered. Missense mutations (mutation in which a single nucleotide is changed) of the gene, and duplications and triplications of the locus containing it have been found in different groups with familial PD. Missense mutations are very rare with few families found in all the world. On the other hand, multiplications of the SNCA locus account for around 2% of familial cases. Multiplications have additionally been found in non symptomatic carriers leading to the conclusion that penetrance is incomplete or age-dependent.
A fragment of the alpha-synuclein is known to be the non-Abeta component of Alzheimer's disease amyloid. Said fragment was originally found in an amyloid-enriched fraction, and identified as a fragment of its precursor protein, NCAP, by cloning of the full-length cDNA. It was later determined that NCAP is the human homologue of Torpedo synuclein. NCAP is now therefore referred to as human alpha-synuclein.
It recently became evident that SNCA expression is an important factor in pathogenesis of PD as increased gene dosage of SNCA leads to familial PD, and polymorphisms in the SNCA promoter increase the risk of developing sporadic PD. SNCA mRNA levels were furthermore found to be increased in individual laser-captured dopaminergic neurons in substantia nigra of PD patients. It seems that already a minor increase of wild-type SNCA protein in the presynaptic compartment of neurons is sufficient to induce dysfunction and degeneration.
Voustinas and colleagues have studied the expression of alleles of the alpha-synuclein gene in a lymphoblastoid cell line and in blood cells of a patient heterozygous for the mutation p.Ala53Thr, the first mutation implicated in PD pathogenesis (Voustinas, G. E. et al. (2010), Allelic imbalance of expression and epigenetic regulation within the alpha-synuclein wild-type and p.Ala53Thr alleles in Parkinson disease, Hum. Mutat. 31(6):685-691). Said patient was diagnosed with early-onset PD, and belonging to a family with multiple PD cases in several generations, with autosomal dominant inheritance and <100% penetrance of the disease. Evidence is provided that SNCA shows monoalleleic expression in this patient, that epigenetic silencing of the mutated allele involves histone modifications but not DNA methylation, because expression of the mutant allele was silenced despite the finding that all analyzed CpG sites were found to be unmethylated, and that steady state mRNA levels deriving from the normal SNCA allele in this patient exceeded those of both normal SNCA alleles in matching control individuals. An imbalanced SNCA expression has thus been documented, with silencing the expression of the p.Ala53Thr allele and upregulation of the expression of the wild-type allele.
Grundemann and colleagues detected significantly elevated alpha-synuclein mRNA levels in individual, surviving neuromelanin- and tyrosine hydroxylase-positive substantia nigra dopaminergic neurons from idiopathic PD brains compared to unaffected controls (Grundemann, J. et al. (2008), Elevated a-synuclein mRNA levels in individual UV-laser-microdissected dopaminergic substantia nigra neurons in idiopathic Parkinson's disease, NAR 36(7): e38). This data demonstrate a cell-type specific transcriptional upregulation of alpha-synuclein expression in neurons being a key population in PD.
It has also been found in in-vitro studies that methylation of human SNCA intron I decreased gene expression, while inhibition of DNA methylation activated SNCA expression. Notably, methylation of SNCA intron I was reduced in DNA from sporadic PD patient's substantia nigra putamen, and cortex (Jowaed, A. et al. (2010), Methylation regulates alpha-synuclein expression and is decreased in Parkinson's disease patients' brains. J. Neurosci, 30(18):6355-6359). Methylation pattern in the SNCA region of interest varied considerably, however, between tissues and individuals.
Besides of its association with Alzheimer's disease and Parkinson's disease, epigenetic regulation of the SNCA gene's expression appears to also be involved in other disorders. For example, an increased methylation of the alpha synuclein promoter DNA in patients with alcoholism was observed (Bonsch, D. et al. (2005), DNA hypermethylation of the alpha synuclein promoter in patients with alcoholism, Neuroreport. 8; 16(2):167-170). The increased methylation of the alpha synuclein promoter DNA was significantly associated with elevated homocysteine levels in said patients. Since hypermethylation of DNA is an important epigenetic factor in down regulation of gene expression, and since alpha synuclein has been linked to craving, hypermethylation of alpha-synuclein promoter DNA was discussed to explain the reduced value of craving under alcohol drinking conditions. In contrast, alpha-synuclein protein expression was found to be significantly higher in patients with alcoholism when compared to healthy controls (Bonsch, D. et al. (2005), Alpha-synuclein protein levels are increased in alcoholic patients and are linked to craving, Alcohol Clin. Res. 29(5):763-765).
Global DNA hypomethylation and DNA hypermethylation of the alpha-synuclein promoter was furthermore observed in females with anorexia nervosa indicating epigenetic contribution to the pathophysiology of eating disorders. In patients with anorexia, a decreased alpha-synuclein expression was associated with DNA hypermethylation of the alpha-synuclein promoter. (Frieling, H. et al. (2007), Global DNA hypomethylation and DNA hypermethylation of the alpha synuclein promoter in females with anorexia nervosa, Mol. Psychiatry 12:229-230).
In an embodiment, the present invention provides a method of using peripheral blood monocytes of a patient to at least one of diagnose and assess a risk of a patient of developing Parkinson's disease which includes obtaining peripheral blood monocytes from the patient, and determining a methylation pattern of the SNCA(−926/−483) region of the SNCA gene of the DNA of the peripheral blood monocytes.
The present invention is described in greater detail below on the basis of embodiments and of the drawings in which:
The Sequence Listing associated with this application is filed in electronic form via EFS-Web and is hereby incorporated by reference into this specification in its entirety. The name of the text file containing the Sequence Listing is Sequence_Listing—18072013. The size of the text file is 357,318 Bytes, and the text file was created on Jul. 18, 2013.
The present invention is based on the surprising findings that a decreased methylation in the 5′ region of the human SNCA gene, which was observed in DNA from cells of the central nervous system of patients having developed Parkinson's disease, can also be found in the DNA obtained from peripheral blood monocytes of patients having developed Parkinson's disease. These findings permit providing an inexpensive and easy to perform test for diagnosis of Parkinson's disease. Such a test is further advantageous, because it permits diagnosis of Parkinson's disease at a very early stage of the disease's progression and may even permit assessing a person's risk of developing Parkinson's disease when becoming older, even if no symptoms are yet present.
In an embodiment, the present invention provides for the use of peripheral blood monocytes of a patient for diagnosis of Parkinson's disease and/or assessing the patient's risk of developing Parkinson's disease, wherein the methylation pattern of the SNCA gene from DNA of said peripheral blood monocytes is determined.
In an embodiment, the present invention provides a method of determining the methylation pattern of the SNCA gene from DNA of peripheral blood monocytes of a patient for diagnosis of Parkinson's disease and/or assessing the patient's risk of developing Parkinson's disease.
In an embodiment, the present invention provides a method for diagnosis and/or assessing a patient's risk of developing Parkinson's disease, wherein the methylation pattern of the SNCA gene from DNA of peripheral blood monocytes of said patient is determined.
The term “patient” refers to any person whose risk of developing Parkinson's disease during his or her lifetime is to be assessed or who is to be diagnosed for Parkinson's disease, regardless of whether clinical symptoms, in particular neurological symptoms being associated with Parkinson's disease, are present or not. The term “patient” is therefore not restricted to persons already affected by Parkinson's disease, but also refers to healthy individuals.
In an embodiment of the present invention, peripheral blood monocytes of a patient are used for diagnosis of whether the patient has developed Parkinson's disease and/or for assessing the patient's risk of developing Parkinson's disease, even if said patient does not shown any neurological symptoms associated with Parkinson's disease. For diagnosis of whether the patient has developed Parkinson's disease and/or for assessing the patient's risk of developing Parkinson's disease, in particular sporadic PD, the methylation pattern of the SNCA gene obtained from genomic DNA of the patient's peripheral blood monocytes is determined.
Using peripheral blood monocytes for diagnosis of whether the patient has developed Parkinson's disease and/or for assessing the patient's risk of developing Parkinson's disease is advantageous over methods currently used for diagnosing Parkinson's disease because peripheral blood monocytes of a patient can be easily obtained without posing undue health hazards to the patient and without the need of expensive technical equipment. Peripheral blood monocytes can moreover be used even if the patient does not suffer from neurological symptoms associated with Parkinson's disease. The present invention therefore provides an opportunity to determine whether a person is at risk of developing PD in the future. It may also be possible to use peripheral blood monocytes from a patient's blood sample that was taken for other reasons than the instant diagnosis or risk assessment. For example, using peripheral blood monocytes from blood samples of a patient that were taken at various points of time during the patient's life, alterations in the methylation pattern of the SNCA gene can be monitored without extensive costs such that the etiology of sporadically occurring PD may be determined.
In an embodiment of the present invention, the use of peripheral blood monocytes of a patient for diagnosing and/or assessing the patient's risk of developing Parkinson's disease is characterized in that the methylation pattern of intron 1 of the SNCA gene from genomic DNA of the patient's peripheral blood monocytes is determined.
In an embodiment of the present invention, the use of peripheral blood monocytes of a patient for diagnosing and/or assessing the patient's risk of developing Parkinson's disease is characterized in that the methylation pattern of the SNCA(−926,−483) region of the human SNCA gene from genomic DNA of the patient's peripheral blood monocytes is determined.
The SNCA(−926,−483) region of the SNCA gene is the nucleotide sequence of the SNCA gene upstream of the ATG start codon for SNCA, consisting of the nucleotides sequence from nucleotide −926 to nucleotide −483 with respect to the ATG start codon of SNCA, the adenosine (A) of said start codon being designated nucleotide 1. The SNCA(−926/−483) region is therefore located upstream or 5′ of the start codon as is identified by the minus in front of the designated position numbers. Notably, intron 1 of the human SNCA gene and hence the SNCA(−926,−483) region of the human SNCA gene does not comprise the promoter of the human SNCA gene. The promoter of the human SNCA gene is located upstream, i.e., in 5′ direction, of exon 1 which in turn is located upstream of and adjacent to said intron 1. The nucleotide sequence of SNCA(−926,−483) region (SEQ ID NO: 1) of the human SNCA gene is shown in
The SNCA(−926,−483) region of the human SNCA gene comprises 23 CpG dinucleotides, wherein the cytosine of each of these CpG dinucleotides may or may not be methylated. Whether the cytosine of a given CpG dinucleotide is methylated or not defines the methylation status of the cytosine of said particular CpG dinucleotide. The methylation pattern of a DNA molecule or a region of a DNA molecule, for example, a gene such as the SNCA gene, or of the SNCA(−926,−483) region of the human SNCA gene, is defined by the combination of the methylation status of each CpG dinucleotide within said DNA molecule or said region. Table 1 provides an overview of the 23 CpG dinucleotides within the SNCA(−926/−483) region of the human SNCA gene and their position within intron 1 with respect to the ATG start codon of the human SNCA gene.
Table 1: List of the 23 CpG dinucleotides within the SNCA(−926/−483) region of the human SNCA gene which may be subject to methylation. The position of each of these 23 CpG dinucleotides with reference to the ATG start codon of the human SNCA gene is provided, said start codon consisting of nucleotides 1 to 3 pursuant to the nomenclature used herein.
In an embodiment of the present invention, the methylation status of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene is determined. Said one or more CpG dinucleotides can, for example, be selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene. Said one or more CpG dinucleotides can, for example, be selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926/−483) region of the human SNCA gene.
CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene can, for example, be selected because it was assessed that the methylation status of these particular CpG dinucleotides is significantly altered in patients suffering from Parkinson's disease, in particular from sporadic PD, compared to healthy control individuals. More specifically, the methylation pattern of the SNCA(−926,−483) region of the human SNCA gene from peripheral blood monocytes as displayed in
In addition, the percentage of methylated CpG dinucleotide No. 2, 11, 12, 18 and 21 of the SNCA(−926,−483) region of the human SNCA gene from peripheral blood monocytes appears to be increased in patients affected with sporadic PD. The evidence is striking although at present not statistically significant due to the low number of probes that were thus far analyzed. However, the methylation pattern of the SNCA(−926,−483) region of the human SNCA gene from peripheral blood monocytes is altered in patients affected by PD in that said methylation pattern displays a hypermethylation with respect to CpG dinucleotide No. 2, 11, 12, 18 and 21 of the SNCA(−926,−483) region of the human SNCA gene from peripheral blood monocytes.
Notwithstanding that virtually any method for analyzing the methylation status of a given CpG dinucleotide can be employed for analyzing the methylation status of the human SNCA gene, of intron 1 of the human SNCA gene, and/or of the SNCA(−926,−483) region of the human SNCA gene, in particular of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene, for example, of one or more CpG dinculeotides of the SNCA(−926,−483) region of the human SNCA gene selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, the methylation status can, for example, be determined by one or more methods selected from the group consisting of methylation specific PCR, direct sequence analysis of bisulfite-treated DNA, COBRA-Assay and analysis of methylation-specific restriction enzyme digestion.
In an embodiment of the present invention, the methylation pattern of the human SNCA-gene, of intron 1 of the human SNCA gene, or of the SNCA(−926,−483) region of the human SNCA gene, in particular of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene, for example, of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene selected from the group consisting of CpG dinucleotides 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926/−483) region of the human SNCA gene is determined by methylation specific PCR (MSP), and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926/−483) region of the human SNCA gene.
In animals, DNA methylation predominantly involves the addition of a methyl group to the carbon-5 position of cytosine residues of the dinucleotide CpG, and is implicated in repression of transcriptional activity. Treatment of DNA with sodium bisulfite converts cytosine residues to uracil, but leaves 5-methylcytosine residues unaffected. Sodium bisulfite treatment thus introduces specific changes in the DNA sequence that depend on the methylation status of individual cytosine residues, yielding single-nucleotide resolution information about the methylation status of a segment of DNA.
MSP can rapidly assess the methylation status of virtually any group of CpG dinucleotides within a CpG island, independent of the use of cloning or methylation-sensitive restriction enzymes. The MSP comprises initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. MSP requires very small quantities of DNA, and is sensitive to 0.1% methylated alleles of a given CpG island locus.
In an embodiment of the present invention, methylation of the human SNCA-gene, of intron 1 of the human SNCA gene, and/or of the SNCA(−926,−483) region of the human SNCA gene, in particular of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene, for example, of one or more CpG dinculeotides of the SNCA(−926,−483) region of the human SNCA gene selected from the group consisting of CpG dinucleotides 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene is determined by sequence analysis of bisulfite treated DNA.
The method of methylation analysis utilizing sequence analysis of bisulfite-treated DNA involves bisulfite treatment of the DNA to be analyzed, PCR amplification of the bisulfite treated DNA, cloning of the amplification product, and standard dideoxynucleotide DNA sequencing of the cloned DNA fragments to directly determine the nucleotides resistant to bisulfite conversion. Primers for PCR amplification can, for example, be designed to be strand-specific but not methylation-specific, i.e., the nucleotide sequence of the preferred primers do not comprise a sequence corresponding to a nucleotide sequence including a CpG dinucleotide. The aforementioned primers for PCR amplification flank do not, for example, involve the methylation site or methylation sites of interest. However, in an additional or alternative embodiment, at least one or both, the forward primer and the reverse primer for PCR amplification may cover one or more CpG dinucleotides. To be strand specific and to allow amplification of methylated as well as non-methylated DNA fragments, a mixture of primers may be utilized, wherein the mixture of strand primers consists of primers having a pyrimidine nucleotide (Y) for the cytosine of the CpG dinucleotide within the DNA fragment to be amplified and covered by said strand primer, i.e., a C for amplification of said DNA fragment which is methylated at said C, or a T for amplification of said DNA fragment which is not methylated at said C. The PCR amplification will therefore amplify both methylated and unmethylated sequences, in contrast to methylation-specific PCR. All sites of unmethylated cytosines are displayed as thymines in the resulting amplified sequence of the sense strand, and as adenines in the amplified antisense strand. This method requires cloning of the PCR products prior to sequencing for adequate sensitivity. Alternatively, nested PCR methods can be used to enhance the product for sequencing.
Pyrosequencing may also be used to analyze bisulfite-treated DNA without using methylation-specific PCR. Following PCR amplification of the region of interest, pyrosequencing is used to determine the bisulfite-converted sequence of specific CpG sites in the region. The ratio of C-to-T at individual sites can be determined quantitatively based on the amount of C and T incorporation during the sequence extension.
In an embodiment of the present invention, methylation of the human SNCA-gene, of intron 1 of the human SNCA gene, or of the SNCA(−926,−483) region of the human SNCA gene, in particular of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene, for example, of one or more CpG dinculeotides of the SNCA(−926,−483) region of the human SNCA gene selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, is determined by combined bisulfite restriction analysis (COBRA assay).
The COBRA assay is a quantitative technique to determine DNA methylation levels at specific gene loci in small amounts of genomic DNA. In the COBRA assay, restriction enzyme digestion is used to reveal methylation dependent sequence differences in PCR products of sodium bisulfite-treated DNA. Methylation levels in the original DNA sample are represented by the relative amounts of digested and undigested PCR product in a linearly quantitative fashion across a wide spectrum of DNA methylation levels. The COBRA assay is easy to use and provides quantitative accuracy.
In the COBRA assay, methylation-dependent sequence differences are introduced into the genomic DNA by sodium bisulfite treatment and subsequent PCR amplification of the bisulfite treated DNA. This combination of bisulfite treatment and PCR amplification results in conversion of unmethylated cytosine residues to thymine and of methylated cytosine residues to cytosine. This sequence conversion can lead to methylation dependent creation of new restriction enzyme sites or it can lead to the methylation dependent retention of pre-existing restriction enzyme sites such as, for example, BstUI (CGCG). The primers used in the PCR amplification reaction do not contain CpG dinucleotides so that the amplification step does not discriminate between templates according to their original methylation status. Therefore, in the mixed population of DNA fragments resulting from said PCR, the fraction that has a newly created or retained restriction site that contains a CpG(s) directly reflects the percentage DNA methylation at that site in the original genomic DNA.
The aforementioned methods, i.e., MSP, direct sequencing of bisulfate-treated DNA, and COBRA, utilize oligonucleotides for analyzing the methylation pattern of a DNA fragment, for example, as primers in PCR amplification reactions. For analyzing the methylation pattern of the human SNCA gene, of intron 1 of the human SNCA gene, or of the of the SNCA(−926,−483) region of the human SNCA gene, for example, of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926/−483) region of the human SNCA gene, and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926/−483) region of the human SNCA gene, one or more oligonucleotides comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 5 to SEQ ID NO: 898 may be used.
Any one of said oligonucleotides comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 5 to SEQ ID NO: 898 may consist of 16, 17, 18, 19, 20, 21, 22 or more nucleotides. Oligonucleotides for use in analyzing the methylation pattern of the human SNCA gene, of intron 1 of the human SNCA gene, or of the of the SNCA(−926,−483) region of the human SNCA gene, for example, of one or more CpG dinculeotides of the SNCA(−926,−483) region of the human SNCA gene selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, can, for example, consist of 18 nucleotides having a nucleotide sequences selected from the group consisting of SEQ ID NO: 5 to SEQ ID NO: 898.
Table 3: Examples of complementary oligonucleotide sequences specific for bisulfite converted methylated and/or non-methylated antisense strand of the SNCA(−926,−483) region of the human SNCA gene.
Within the nucleotide sequences set forth in Table 1, “Y” represents C or T, wherein Y=C is specific for a methylated cytosine in the non-bisulfite converted DNA of the SNCA(−926,−483) region of the human SNCA gene, and Y=T is specific for a non-methylated cytosine of a CpG dinucleotide in the non-bisulfite converted DNA of the SNCA(−926,−483) region of the human SNCA gene.
Within the nucleotide sequences set forth in Table 2, “R” represents G or A, wherein R=G is specific for a methylated cytosine in the non-bisulfite converted DNA of the SNCA(−926/−483) region of the human SNCA gene, and R=A is specific for a non-methylated cytosine of a CpG dinucleotide in the non-bisulfite converted DNA of the SNCA(−926,−483) region of the human SNCA gene.
For amplification reactions of the SNCA(−926,−483) region of the human SNCA gene or at least of portions of SNCA(−926,−483) region of the human SNCA gene comprising at least one of the 23 CpG dinucleotides present in the SNCA(−926,−483) region of the human SNCA gene, the forward oligonucleotide primer can, for example, be selected from the group of oligonucleotides comprising or consisting of the nucleotide sequences selected from the group consisting of SEQ ID NO. 5 to SEQ ID NO: 451. For amplification reactions of the SNCA(−926/−483) region of the human SNCA gene or at least of portions of SNCA(−926/−483) region of the human SNCA gene comprising at least one of the 23 CpG dinucleotides present in the SNCA(−926/−483) region of the human SNCA gene, the reverse oligonucleotide primer can, for example, be selected from the group of oligonucleotides comprising or consisting of the nucleotide sequences selected from the group consisting of SEQ ID NO. 452 to SEQ ID NO: 898.
A primer for sequence analysis of the cloned PCR products from bisulfite converted DNA from the SNCA(−926,−483) region of the human SNCA gene can, for example, be selected from the group of oligonucleotides comprising or consisting of the nucleotide sequences selected from the group consisting of SEQ ID NO. 5 to SEQ ID NO: 451 and SEQ ID NO. 452 to SEQ ID NO: 898.
In an embodiment of the present invention, methylation of the human SNCA-gene, of intron 1 of the human SNCA gene, and/or of the SNCA(−926,−483) region of the human SNCA gene, in particular of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene, for example, of one or more CpG dinculeotides of the SNCA(−926,−483) region of the human SNCA gene selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, is determined by analyzing restriction enzyme digestions.
Analyzing restriction enzyme digestion of DNA to analyze the methylation status of said DNA is based on the property of some restriction enzymes to be unable to cut methylated DNA. Since in eukaryotic DNA only cytosine in CG context can be methylated, restriction enzymes with CG sequences within their restriction sites come may be used. Two classical enzyme pairs are, for example, HpaII-MspI (CCGG) and SmaI-XmaI (CCCGGG). Both enzymes of each pair recognize nucleotides sequences comprising a CCGG sequence. HpaII and SmaI are, however, unable to cut DNA when the internal cytosine is methylated. This property makes HpaII-MspI and SmaI-XmaI valuable tools for rapid methylation analysis.
Prior to the methylation analysis by restriction enzyme digestion, the nucleotide sequence of the DNA fragment to be investigated has to be analyzed for the presence of CpG dinucleotides and specific restriction sites for enzyme pairs wherein one isoschizomer hydrolyses the DNA even if the cytosine of the CpG dinucleotide within the recognition sequence is methylated, and wherein the other isoschizomer does not. After restriction enzyme digestion, the DNA fragments will be separated by gel electrophoresis. A Southern blot hybridization of the separated DNA fragments has to be performed, wherein the probe for used for Southern blot hybridization should be located within the region to be analyzed and cover it completely or at least partially.
In an embodiment of the present invention, a method of determining the methylation pattern of the human SNCA gene for diagnosing and/or assessing a patient's risk of developing Parkinson's disease is provided, in particular of developing sporadic PD, wherein the SNCA gene is obtained from DNA of peripheral blood monocytes of said patient. The method according to the embodiment permits the establishment of a method for diagnosing Parkinson's disease, even if no neurological symptoms associated with Parkinson's disease are present in the patient yet. The method according to the embodiment of the present invention as well as the diagnostic assay that is based on the method according to an embodiment of the present invention are inexpensive and easy to perform without affecting the patient's acceptance.
In an embodiment of the method according to the present invention, the methylation pattern of intron 1 of the human SNCA gene from genomic DNA of the patient's peripheral blood monocytes can, for example, be determined.
In an embodiment of the method according to the present invention, the methylation pattern of the SNCA(−926,−483) region of the human SNCA gene from genomic DNA of the patient's peripheral blood monocytes can, for example, be determined.
In an embodiment of the method according to the present invention, the methylation status of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene can, for example, be determined. Said one or more CpG dinucleotides can, for example, be selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene. Said one or more CpG dinucleotides can, for example, be selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene.
Notwithstanding that virtually any method for analyzing the methylation status of a given CpG dinucleotide can be employed for analyzing the methylation pattern of the human SNCA gene, of intron 1 of the human SNCA gene, and/or of the SNCA(−926,−483) region of the human SNCA gene, in particular of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene, one or more CpG dinculeotides of the SNCA(−926,−483) region of the human SNCA gene can, for example, be selected from the group consisting of CpG dinucleotides 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, and, for example, said one or more CpG dinucleotides is/are selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926/−483) region of the human SNCA gene, the methylation status can, for example, be determined by one or more methods selected from the group consisting of methylation specific PCR, direct sequence analysis of bisulfite-treated DNA, COBRA-Assay and methylation-specific restriction enzyme digestion as described in more detail herein above.
In an embodiment of the method according to the present invention, methylation of the human SNCA-gene, of intron 1 of the human SNCA gene, and/or of the SNCA(−926,−483) region of the human SNCA gene, in particular of one or more CpG dinucleotides of the SNCA(−926/−483) region of the human SNCA gene can, for example, be determined by methylation specific PCR (MSP). Said one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene can, for example, be selected from the group consisting of CpG dinucleotides 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, and, for example, said one or more CpG dinucleotides is/are selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926/−483) region of the human SNCA gene,
In an embodiment of the method according to the present invention, methylation of the human SNCA-gene, of intron 1 of the human SNCA gene, and/or of the SNCA(−926,−483) region of the human SNCA gene, in particular of one or more CpG dinucleotides of the SNCA(−926/−483) region of the human SNCA gene can, for example, be determined by sequence analysis of bisulfite treated DNA. Said one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene can, for example, be selected from the group consisting of CpG dinucleotides 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, and, for example, said one or more CpG dinucleotides is/are selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926/−483) region of the human SNCA gene,
In an embodiment of the method according to the present invention, methylation of the human SNCA-gene, of intron 1 of the human SNCA gene, and/or of the SNCA(−926,−483) region of the human SNCA gene, in particular of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene can, for example, be determined by combined bisulfite restriction analysis (COBRA assay). Said one or more CpG dinucleotides of the SNCA(−926/−483) region of the human SNCA gene can, for example, be selected from the group consisting of CpG dinucleotides 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, and, for example, said one or more CpG dinucleotides is/are selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926/−483) region of the human SNCA gene.
In an embodiment of the method according to the present invention, methylation of the human SNCA-gene, of intron 1 of the human SNCA gene, and/or of the SNCA(−926,−483) region of the human SNCA gene, in particular of one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene can, for example, be determined by analyzing restriction enzyme digestions. Said one or more CpG dinucleotides of the SNCA(−926,−483) region of the human SNCA gene can, for example, be selected from the group consisting of CpG dinucleotides 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene, and, for example, said one or more CpG dinucleotides is/are selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926/−483) region of the human SNCA gene.
In an embodiment, the present invention further comprises a method for diagnosis and/or assessment of a patient's risk of developing Parkinson's disease, in particular sporadic PD, wherein said diagnostic method comprises analysis of the methylation pattern of the human SNCA gene from DNA of peripheral blood monocytes, said peripheral blood monocytes being obtained from said patient.
The method for diagnosing Parkinson's disease and/or assessing a patient's risk of developing Parkinson's disease according to an embodiment of the present invention may comprise obtaining a blood sample from said patient. Said blood sample may be specifically obtained for diagnosing Parkinson's disease or assessing the patient's risk of developing Parkinson's disease. Alternatively, blood samples of said patient may be used which were obtained from said patient for other reasons and/or earlier, wherein said blood sample had to be stored under appropriate conditions which prevent the genomic DNA from the peripheral blood monocytes of said blood sample from becoming degraded.
The method according to an embodiment of the present invention comprises isolating of peripheral blood monocytes from the patient's blood sample or blood samples. The method according to the emboiment of the present invention further comprises isolating genomic DNA from the patient's peripheral blood monocytes, and determining the methylation pattern of the patient's SNCA gene, for example, the methylation pattern of intron 1 of the patient's SNCA gene, for example, the methylation pattern of the SNCA(−926/−483) region of the patient's SNCA gene. In an embodiment of the method according to the present invention, the methylation status of one or more CpG dinucleotides of the SNCA(−926/−483) region of the patient's SNCA gene can, for example, be determined. The methylation status of one or more CpG dinucleotides can, for example, be determined, wherein said one or more CpG dinucleotides is/are selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the patient's SNCA gene is determined, and, for example, said one or more CpG dinucleotides is/are selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the human SNCA gene.
Determining the methylation pattern of the patient's SNCA gene, of intron 1 of the patient's SNCA gene, and/or of the SNCA(−926,−483) region of the patient's SNCA gene, more specifically the methylation status of one or more CpG dinucleotides of the SNCA(−926,−483) region of the patient's SNCA gene, one or more CpG dinucleotides of the SNCA(−926,−483) region of the patient's SNCA gene can, for example, be selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the patient's SNCA gene, and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the patient's SNCA gene, may utilize virtually any technique that is suitable for analyzing a DNA's methylation status. However, according to an embodiment of the method according to the present invention, the methylation status is determined by one or more methods selected from the group consisting of methylation specific PCR, sequence analysis of bisulfite-treated DNA, COBRA-Assay and methylation-specific restriction patterns.
In an embodiment, the method according to the present invention further comprises comparing the methylation pattern of the patient's SNCA gene, of intron 1 of the patient's SNCA gene, and/or of the SNCA(−926,−483) region of the patient's SNCA gene, more specifically the methylation status of one or more CpG dinucleotides of the SNCA(−926,−483) region of the patient's SNCA gene, for example, of one or more CpG dinucleotides of the SNCA(−926/−483) region of the patient's SNCA gene selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the patient's SNCA gene, and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the patient's SNCA gene, with the methylation status of the corresponding SNCA gene, intron, region and/or CpG dinucleotide(s) of healthy individuals.
In an embodiment, the method according to the present invention further comprises comparing the methylation pattern of the patient's SNCA gene, of intron 1 of the patient's SNCA gene, and/or of the SNCA(−926,−483) region of the patient's SNCA gene, more specifically of one or more CpG dinucleotides of the SNCA(−926,−483) region of the patient's SNCA gene, for example, the methylation status of one or more CpG dinucleotides of the SNCA(−926/−483) region of the patient's SNCA gene selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the patient's SNCA gene, and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the patient's SNCA gene, from DNA of a blood sample obtained from the patient at a given point of time with the methylation status of the corresponding gene, intron, region and/or CpG dinucleotide(s) from DNA of one or more further blood samples of the same patient, wherein said one or more further blood sample(s) was/were obtained at different points of time than said blood sample obtained from the patient at said given point of time. This embodiment permits to monitor alterations in the methylation pattern of the patient's SNCA gene, and/or of the SNCA(−926,−483) region of the patient's SNCA gene, more specifically of one or more CpG dinucleotides of the SNCA(−926,−483) region of the patient's SNCA gene, for example, of one or more CpG dinucleotides of the SNCA(−926,−483) region of the patient's SNCA gene selected from the group consisting of CpG dinucleotides No. 1, 2, 7, 8, 11, 12, 13, 18, 21, 22 and 23 of the SNCA(−926,−483) region of the patient's SNCA gene, and, for example, of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the patient's SNCA gene, over time, and may enable to elucidating the etiology of Parkinson's disease and/or monitoring progression or regression of Parkinson's disease of a patient.
The method according to the present invention further comprises determining whether the patient's SNCA gene, intron 1 of the patient's SNCA gene, or the SNCA(−926,−483) region of the patient's SNCA gene is hypomethylated compared to the corresponding gene, intron or region of the SNCA gene from healthy individuals. Hypomethylation of the patient's SNCA gene, of intron 1 of the patient's SNCA gene, or of the SNCA(−926,−483) region of the patient's SNCA gene may be determined in that the methylation status of one or more CpG dinucleotides of the SNCA(−926,−483) region of the patient's SNCA gene is compared to the methylation status of the corresponding CpG dinucleotide(s) of the SNCA(−926,−483) region from healthy individuals. In an embodiment, hypomethylation can, for example, be determined in that the methylation status of one or more CpG dinucleotides of the SNCA(−926,−483) region of the patient's SNCA gene selected from the group consisting of CpG dinucleotides No. 1, 7, 8, 13, 22 and 23 of the SNCA(−926,−483) region of the patient's SNCA gene is compared to the methylation status of the corresponding CpG dinucleotide(s) of the SNCA(−926,−483) region from healthy individuals.
In determining whether the patient's SNCA gene, intron 1 of the patient's SNCA gene or the SNCA(−926,−483) region of the patient's SNCA gene is hypomethylated compared to the corresponding gene, intron or region of healthy individuals it can be deduced whether the patient is at risk of developing Parkinson's disease even if neurological symptoms are absent, or whether the patient already has Parkinson's disease even no neurological symptoms are present or only present mildly and yet non-specifically.
In an embodiment of the present invention, the method comprises determining whether the patient's SNCA gene, intron 1 of the patient's SNCA gene, or the SNCA(−926,−483) region of the patient's SNCA gene is hypermethylated with respect to particular CpG dinucleotides within said SNCA gene, said intron 1 or said SNCA(−926,−483) region compared to the corresponding gene, intron or region of the SNCA gene from healthy individuals. Hypermethylation of said SNCA gene, said intron 1 or said SNCA(−926,−483) region with respect to particular CpG dinucleotides therein may be determined in that the methylation status of one or more CpG dinucleotides of the SNCA(−926,−483) region of the patient's SNCA gene is compared to the methylation status of the corresponding CpG dinucleotide(s) of the SNCA(−926/−483) region from healthy individuals. In an embodiment, hypermethylation can, for example, be determined in that the methylation status of one or more CpG dinucleotides selected from the group consisting of CpG dinucleotides No. 2, 11, 12, 18 and 21 of the SNCA(−926,−483) region of the patient's SNCA gene is/are compared to the methylation status of the corresponding CpG dinucleotide(s) of the SNCA(−926,−483) region from healthy individuals.
In determining whether the patient's SNCA gene, intron 1 of the patient's SNCA gene or the SNCA(−926,−483) region of the patient's SNCA gene is hypermethylated with respect to particular CpG dinucleotides within the SNCA gene, intron 1 of the SNCA gene or the SNCA(−926/−483) region compared to the corresponding gene, intron or region of healthy individuals it can be deduced whether the patient is at risk of developing Parkinson's disease even if neurological symptoms are absent, or whether the patient already has Parkinson's disease even no neurological symptoms are present or only present mildly and yet non-specifically.
The present invention will now be described with respect to particular embodiments and with reference to the Figures, however, the present invention is not limited thereto. The drawings described are only schematic and are non-limiting.
Peripheral blood monocytes were isolated from blood samples of 19 patients suffering from sporadic PD and 20 healthy individuals. DNA isolation and bisulfite treatment of the isolated DNA were performed as described by Pieper et al. (Pieper, H. C. et al. (2008), Different methylation of the TNF-alpha promoter in cortex and substantia nigra: implications for selective neuronal vulnerability, Neurobiol. Dis. 32:521-527).
Bisulfite treated DNA was amplified using SNCA—For (SEQ ID NO: 2) and SNCA-Rev (SEQ ID NO: 3), specifically designed for bisulfite treated SNCA(−926/−483) DNA. PCR products were cloned into pCR 2.1 TOPO vector (Invitrogen) following the manufacturer's instructions. Plasmid DNA was isolated from at least ten clones per individual, and sequenced using vector specific primer M13reverse (CAGGAAACAGCTATGAC; SEQ ID NO: 4) and the Big Dye Terminator v1.1 Cycle Sequencing Kit (Applied Biosystems) and analyzed on an ABI PRISM 310 Genetic Analyzer.
The results of determining the methylation pattern of the SNCA(−926/−483) DNA from lymphocytes of healthy individuals and PD patients is shown in
Overall, methylation of the human SNCA gene from peripheral blood monocytes, in particular of intron 1 of the human SNCA genes, and more specifically of the SNCA(−926,−483) region, is reduced in PD patients compared to control. Linear regression analysis furthermore denoted a trend towards hypomethylation with increased age in PD patients.
While the present invention has been illustrated and described in detail in the drawings and foregoing description, such illustration and description are to be considered illustrative or exemplary and not restrictive; the present invention is not limited to the disclosed embodiments. Other variations to the disclosed embodiments can be understood and effected by those skilled in the art in practicing the present invention, from a study of the drawings, the disclosure, and the appended claims. In the claims, the word “comprising” does not exclude other elements or steps, and the indefinite article “a” or “an” does not exclude a plurality. The mere fact that certain measures are recited in mutually different dependent claims does not indicate that a combination of these measures cannot be used to advantage. Any reference signs in the claims should not be construed as limiting the scope.
| Number | Date | Country | Kind |
|---|---|---|---|
| 11152285.0 | Jan 2011 | EP | regional |
This application is a U.S. National Phase application under 35 U.S.C. §371 of International Application No. PCT/EP2012/051260, filed on Jan. 26, 2012 and which claims benefit to European Patent Application No. 11152285.0, filed on Jan. 26, 2011. The International Application was published in English on Aug. 2, 2012 as WO 2012/101228 A1 under PCT Article 21(2).
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/EP12/51260 | 1/26/2012 | WO | 00 | 7/25/2013 |
